Genomic differentiation
Mitochondrial and nuclear phylogenies (Fig. 2d) show strong support for two reciprocally monophyletic species: M. americana and M. caurina. Both trees also show support for an insular M. caurinaclade (QCI, ADM). The placement of the two continental M. caurina(COL, PNW) differed in the two phylogenies, but they were strongly supported as distinct from the insular M. caurina , suggesting substantial genomic divergence between continental and insular M. caurina . Two individuals (KUI, MTX) exhibited cytonuclear discordance. PCA results (Fig. 2a-c) are consistent with our nuclear phylogeny, demonstrating substantial divergence not only between New WorldMartes species (PC1 = 46%; Fig. 2b), but also between insular and continental populations of M. caurina (PC1 = 39%; Fig. 2c). Within M. caurina, PC2 also separates mainland M. caurinapopulations (COL, PNW) and accounts for a notable 34% of the variation. PCA plots (Fig. 2a-c) highlight the intermediacy of putative hybrid individuals (KUI, MTX) and also their distinction from each other.
The inbreeding coefficient, FIS, is highest for insularM. caurina : 0.89 for ADM and 0.77 for QCI (Supplemental Information 4). Mainland M. caurina also exhibit high FIS, 0.65 for PNW and 0.62 for COL, followed by populations of M. americana. CHI has the lowest FIS of all M. americana populations and the 2 putative hybrid individuals have an FIS of essentially 0. FST was 0.438 between pooled M. americana and pooled M. caurina . Contrasting pooled M. americana against pooled (insular and mainland) populations of M. caurina found similar, high FST estimates (mean = 0.44-0.45, weighted mean = 0.68-0.70) with only moderate FST estimates between insular and continental populations of M. caurina (mean = 0.01, weighted mean = 0.11; Supplemental Information5).F2- statistics (Supplemental Information 6) and FS(local inbreeding or relatedness2, Supplemental Information 7) demonstrate similar patterns of genetic differentiation between individuals and species, highlighting divergence within M. caurina . Nucleotide diversity (π) was similar across species, but analysis of insular and mainland M. caurina populations separately produced elevated π estimates, with the highest values for insular M. caurina (Supplemental Information 8). Insular M. caurina also exhibited the highest positive D value, with mainland M. caurina exhibiting only negative and the lowest median D value (Supplemental Information 8).